Biophysics for Beginners: A Journey through the Cell Nucleus, 2nd Edition
- Length: 528 pages
- Edition: 2
- Language: English
- Publisher: Jenny Stanford Publishing
- Publication Date: 2021-11-18
- ISBN-10: 9814877808
- ISBN-13: 9789814877800
- Sales Rank: #4997227 (See Top 100 Books)
Biophysics is a new way of looking at living matter. It uses quantitative experimental, theoretical, and computational methods, thereby opening a new window for studying and understanding life processes. This textbook provides a brief introduction to the basics of the field, followed by in-depth discussions of more advanced biophysics subjects, going all the way to state-of-the-art experiments and their theoretical interpretations. The second edition presents some of the newest developments in the field (e.g., biomolecular condensates, loop extrusion), a new chapter on computational methods, and many computer exercises specially designed for this textbook.
Cover Half Title Title Page Copyright Page Table of Contents Preface to the First Edition Preface to the Second Edition Chapter 1: Molecular Biology of the Cell 1.1: The Central Dogma of Molecular Biology 1.2: A Journey through the Cell Nucleus Chapter 2: Statistical Physics 2.1: The Partition Function 2.2: Applications 2.3: The Entropy 2.4: Particles with Interactions and Phase Transitions 2.5: Biomolecular Condensates Chapter 3: Polymer Physics 3.1: Random Walks 3.2: Freely Jointed and Freely Rotating Chains 3.3: The Role of Solvent Quality 3.4: Self-Avoiding Walks 3.5: The Flory Argument 3.6: The Blob Picture 3.7: Polymers in Poor Solvents 3.8: Internal Structure of Polymers Chapter 4: DNA 4.1: The Discovery of the DNA Double Helix 4.2: DNA on the Base Pair Level 4.2.1: A Geometrical Approach 4.2.2: A Statistical Physics Approach 4.3: DNA as a Wormlike Chain 4.4: DNA Melting Chapter 5: Stochastic Processes 5.1: Introduction 5.2: Markov Processes 5.3: Master Equation 5.4: Fokker–Planck Equation 5.5: Application: Escape over a Barrier 5.6: Application: Dynamic Force Spectroscopy 5.7: Langevin Equation 5.8: Application: Polymer Dynamics Chapter 6: RNA and Protein Folding 6.1: RNA Folding 6.2: Protein Folding Chapter 7: Electrostatics inside the Cell 7.1: Poisson–Boltzmann Theory 7.2: Electrostatics of Charged Surfaces 7.3: Electrostatics of Cylinders and Spheres 7.4: Debye–Hückel Theory 7.5: Breakdown of Mean Field Theory Chapter 8: DNA–Protein Complexes 8.1: Protein Target Search 8.2: RNA Polymerase 8.3: Nucleosome Dynamics 8.3.1: Site Exposure Mechanism 8.3.2: Force-Induced Nucleosome Unwrapping 8.3.3: Nucleosome Sliding 8.4: Chromatin Fibers 8.4.1: Two-Angle Model 8.4.2: Solenoid-Type Models 8.5: Chromatin at Large Scales 8.5.1: From Classical Polymers to Fractal Globules 8.5.2: From Polymer Rings to Loop Extrusion Chapter 9: Computational Methods 9.1: Molecular Dynamics Simulations 9.2: Monte Carlo Simulations Appendix A: Probability Theory Appendix B: The Distribution of Magnetization and the Central Limit Theorem Appendix C: Connection between Polymer Statistics and Critical Phenomena Appendix D: Hamilton’s Principle and the Pendulum Appendix E: Fourier Series Appendix F: The Pre-Averaging Approximation Appendix G: Interaction between Two Equally Charged Plates at Zero Temperature Appendix H: Geometries of Chromatin Fiber Models References Index
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